I use UltraTax for corporate and partnership work.
I also have found the software versions of basis miss or ignore the interactions between debt and equity basis. (Or I don't get the software developer's train of thought.) So I track basis on spreadsheets. The contractors I work for try to keep equity at a certain level or increase it for bonding purposes. Likewise, any additional investment is classified as debt so that it may be withdrawn/repaid without affecting equity. At least, we minimize "conversations" that would run between the bonding company, the bonding agent, and the client during the short construction season.
Thanks to 168(k) the taxable income and loss vary widely from year to year.
So, having the basis calculated by the software, at the individual level; with tracking of unused losses would provide this sole practitioner "another set of eyes" with which to compare with my spreadsheet.
However, I am using 6198 to limit losses due to basis. And my original question was: should I be aware of any issues by using the Form 6198 limitation that ProSeries provides. Other than loans from related parties and loans with the entity as collateral I am not aware of any other differences that a small corporation would have.
I would do corporate returns with ProSeries, but last time I checked one could not run state depreciation schedules for the current and future year in ProSeries.